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Prediction results retrieved after performance evaluation of WHO approved 34 primers to estimate their binding affinities for 3892 SARS-CoV-2 variants.

Lineage (WHO label)	Target Gene	Primer Name	Primer Sequence	Primer Length	Primer GC Content (%)	Start Position	End Position	Primer Direction	ΔG (cal)	Primer first used
GJ.1.2.7	N	US-CDC-N-2	GCGCGACATTCCGAAGAA	18	55.56	29230	29213	R	-21404.2	US
GJ.1.2.7	N	US-CDC-N-3	TGTAGCACGATTGCAGCATTG	21	47.62	28752	28732	R	-23779.6	US
GJ.1.2.7	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-19874.5	Singapore
GJ.1.2.7	N	Corman-N	GAGGAACGAGAAGAGGCTTG	20	55	28833	28814	R	-22527.5	Germany
GJ.1.2.7	N	Won-N	GTTGCGACTACGTGATGAGG	20	55	28849	28830	R	-23088.1	South Korea
GJ.1.2.7	N	NIID-JP-N	TGGCAGCTGTGTAGGTCAAC	20	55	29282	29263	R	-20522.3	Japan
GJ.1.2.7	N	HKU-N	CGAAGGTGTGACTTCCATG	19	52.63	29254	29236	R	-20936.4	Hong Kong
GJ.1.2.7	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
GJ.1.2.7	N	SC2	CCTTGTGTGGTCTGCATGAGTTTAG	25	48	29554	29530	R	-26482.3	US
GJ.1.2.7	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
GJ.1.2.7	ORF1ab	NIID WH-1 F509R854	CAGAAGTTGTTATCGACATAGC	22	40.91	837	816	R	-21257.9	Japan
GJ.1.2.7	ORF1ab	NIID WH-1 Seq F519R840	GACATAGCGAGTGTATGCC	19	52.63	823	805	R	-20165.2	Japan
GJ.1.2.7	S	WuhanCoV-spk1	TGTGGTTCATAAAAATTCCTTTGTG	25	32	24900	24876	R	-23857.7	Japan
GJ.1.2.7	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
GJ.1.2.7	S	NIID WH-1 Seq F24383R24865	CAAAGACACCTTCACGAGG	19	52.63	24848	24830	R	-20677.6	Japan
HK.3.9	ORF1ab	Yip-ORF1ab	TTGTTATAGCGGCCTTCTGT	20	45	1970	1951	R	-21075.5	China
HK.3.9	ORF1ab	Pasteur-ORF1ab-1	CTCCCTTTGTTGTGTTGT	18	44.44	12797	12780	R	-15630.5	France
HK.3.9	ORF1ab	Pasteur-ORF1ab-2	CTGGTCAAGGTTAATATAGG	20	40	14186	14167	R	-18348.8	France
HK.3.9	ORF1ab	CN-CDC-ORF1ab	ACGATTGTGCATCAGCTGA	19	47.37	13460	13442	R	-20306.2	China
HK.3.9	ORF1ab	Young-ORF1ab	CACTTAATGTAAGGCTTTGTTAAG	24	33.33	14243	14220	R	-22408	Singapore
HK.3.9	ORF1ab	Charité-ORF1b	CARATGTTAAASACACTATTAGCATA	26	23.08	15530	15505	R	-9191.15	Germany
HK.3.9	ORF1ab	Won-ORF1ab	TGCATTAACATTGGCCGTGA	20	45	15558	15539	R	-21175.8	South Korea
HK.3.9	ORF1ab	Chan-ORF1ab	GTGTGATGTTGAWATGACATGGTC	24	41.67	16353	16330	R	-17292.3	China
HK.3.9	ORF1ab	HKU-ORF1b	AACRCGCTTAACAAAGCACTC	21	42.86	18909	18889	R	-17655.9	Hong Kong
HK.3.9	S	Young-S	ATCCAGCCTCTTATTATGTTAGAC	24	37.5	21876	21853	R	-22070.7	Singapore
HK.3.9	S	Chan-S	CAAGCTATAACGCAGCCTGTA	21	47.62	22869	22849	R	-18804.3	China
HK.3.9	S	Won-S	CACCTGTGCCTGTTAAACCA	20	50	23213	23194	R	-21965.9	South Korea
HK.3.9	E	Won-E	CACACAATCGATGCGCAGTA	20	50	26365	26346	R	-19261.4	South Korea
HK.3.9	E	Charité-E	ATATTGCAGCAGTACGCACACA	22	45.45	26381	26360	R	-23527.6	Germany
HK.3.9	E	Huang-E	GCAGCAGTACGCACACAATC	20	55	26376	26357	R	-23540.5	China
HK.3.9	E	Niu-E	CACGTTAACAATATTGCAGC	20	40	26391	26372	R	-3779.86	China
HK.3.9	N	CN-CDC-N	CAGACATTTTGCTCTCAAGCTG	22	45.45	28979	28958	R	-23140.2	China
HK.3.9	N	NIH-TH_N	CCCCACTGCGTTCTCCATT	19	57.89	28376	28358	R	-3370.08	Thailand
HK.3.9	N	US-CDC-N-1	TCTGGTTACTGCCAGTTGAATCTG	24	45.83	28358	28335	R	-25148.4	US
HK.3.9	N	US-CDC-N-2	GCGCGACATTCCGAAGAA	18	55.56	29230	29213	R	-21404.2	US
HK.3.9	N	US-CDC-N-3	TGTAGCACGATTGCAGCATTG	21	47.62	28752	28732	R	-23779.6	US
HK.3.9	N	Young-N	AGCACCATAGGGAAGTCC	18	55.56	28648	28631	R	-19874.5	Singapore
HK.3.9	N	Corman-N	GAGGAACGAGAAGAGGCTTG	20	55	28833	28814	R	-22527.5	Germany
HK.3.9	N	Won-N	GTTGCGACTACGTGATGAGG	20	55	28849	28830	R	-23088.1	South Korea
HK.3.9	N	NIID-JP-N	TGGCAGCTGTGTAGGTCAAC	20	55	29282	29263	R	-20522.3	Japan
HK.3.9	N	HKU-N	CGAAGGTGTGACTTCCATG	19	52.63	29254	29236	R	-20936.4	Hong Kong
HK.3.9	N	Chan-N	TTGGATCTTTGTCATCCAATTTG	23	34.78	29306	29284	R	-21867.4	China
HK.3.9	N	SC2	CCTTGTGTGGTCTGCATGAGTTTAG	25	48	29554	29530	R	-26482.3	US
HK.3.9	ORF1ab	NIID WH-1 F501R913	CTTTACCAGCACGTGCTAGAAGG	23	52.17	896	874	R	-25657.5	Japan
HK.3.9	ORF1ab	NIID WH-1 F509R854	CAGAAGTTGTTATCGACATAGC	22	40.91	837	816	R	-21257.9	Japan
HK.3.9	ORF1ab	NIID WH-1 Seq F519R840	GACATAGCGAGTGTATGCC	19	52.63	823	805	R	-20165.2	Japan
HK.3.9	S	WuhanCoV-spk1	TGTGGTTCATAAAAATTCCTTTGTG	25	32	24900	24876	R	-23857.7	Japan
HK.3.9	S	NIID WH-1 F24381R24873	ATTTGAAACAAAGACACCTTCAC	23	34.78	24856	24834	R	-22193.2	Japan
HK.3.9	S	NIID WH-1 Seq F24383R24865	CAAAGACACCTTCACGAGG	19	52.63	24848	24830	R	-20677.6	Japan
EG.6.1.1	ORF1ab	Yip-ORF1ab	TTGTTATAGCGGCCTTCTGT	20	45	1970	1951	R	-21075.5	China
Lineage (WHO label)	Target Gene	Primer Name	Primer Sequence	Primer Length	Primer GC Content (%)	Start Position	End Position	Primer Direction	ΔG (cal)	Primer first used